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Recent Releases of genome-portal

genome-portal - Swedish Reference Genome Portal v1.5.2

Notable content

  • Improve alignment of the text between species cards on the home page.

This release is archived on Zenodo: https://doi.org/10.5281/zenodo.14049736

List of merged pull requests since v1.5.1

Full Changelog: v1.5.1...v1.5.2

- Python
Published by RMCrean 8 months ago

genome-portal - Swedish Reference Genome Portal v1.5.1

Notable content

  • Fix bug in dbxref plugin that affected rendering of tracks in JBrowse
  • Apply dbxref plugin to additional species that have tracks with dbxref annotations (L. tenue, Blastobotrys spp.)
  • Support dbxref linkout to four additional databases (Reactome, AntiFam, KEGG, MetaCyc)
  • Change the front page to show 8 species at a time. This makes the Show All button appear below the pagination bar since the current number of species > 8.

This release is archived on Zenodo: https://doi.org/10.5281/zenodo.14049736

List of merged pull requests since v1.5.0

Full Changelog: v1.5.0...v1.5.1

- Python
Published by brinkdp 9 months ago

genome-portal - Swedish Reference Genome Portal v1.5.0

Notable content

  • Add one new species: European Green Toad (Bufotes viridis)

  • Support for clickable dbxref links in the feature details side-panel of JBrowse 2 through a custom plugin. In short, this means that if a genetic feature has annotations that refer to an accession number in the InterPro, Gene Ontology, and UniProt databases, the user can click on a link to open the database entry in a new tab. The plugin was designed based on this example from the JBrowse 2 documentation.

  • Added a button to toggle display of all species in a single page instead of pagination. The button also displays the total number of species in the portal.

Developer tools

  • Refactored the add_new_species script to a Python package to improve maintainability and data flow. The package takes user submitted forms and automates a large part of the creation of the pages for the new species. (Processing of data tracks is still handled by other tools, though).

This release is archived on Zenodo: https://doi.org/10.5281/zenodo.14049736

List of merged pull requests since v1.4.0

Full Changelog: v1.4.0...v1.5.0

- Python
Published by brinkdp 9 months ago

genome-portal - Swedish Reference Genome Portal v1.4.0

Notable content

  • Add three new species: the yeasts Blastobotrys illinoisensis NRRL YB-1343, Blastobotrys malaysiensis NRRL Y-6417, and Blastobotrys mokoenaii NRRL Y-27120

Developer tools

  • Change the default tabix index format from TBI to CSI indices to accomodate data tracks for genome assemblies that contain very long scaffolds
  • Improve error handling for the GBIF distribution map, and add support to omitt the map for species that do not have any observations (mainly microbial eukaryotes)
  • Update the helper script for generating JBrowse 2 defaultSession configurations with new functionalities and bugfixes

This release is archived on Zenodo: https://doi.org/10.5281/zenodo.14049736

List of merged pull requests since v1.3.3

Full Changelog: https://github.com/ScilifelabDataCentre/genome-portal/compare/v1.3.3...v1.4.0

- Python
Published by brinkdp 9 months ago

genome-portal - Swedish Reference Genome Portal v1.3.3

Notable content

  • Allow iframing of the genome-portal for selected websites, with a new path that makes embedding the genome browser page easier.
  • Update broken links on P. mnemosyne front page.
  • Add documentation on our release strategy.

This release is archived on Zenodo: https://doi.org/10.5281/zenodo.14049736

List of merged pull requests since v1.3.2

Full Changelog: https://github.com/ScilifelabDataCentre/genome-portal/compare/v1.3.2...v1.3.3

- Python
Published by RMCrean 10 months ago

genome-portal - Swedish Reference Genome Portal v1.3.2

Notable content

  • Bump JBrowse Web version to latest (3.2.0)

This release is archived on Zenodo: https://doi.org/10.5281/zenodo.14049736

List of merged pull requests since v1.3.1

Full Changelog: https://github.com/ScilifelabDataCentre/genome-portal/compare/v1.3.1...v1.3.2

- Python
Published by RMCrean 11 months ago

genome-portal - Swedish Reference Genome Portal v1.3.1

Notable content

  • The contact form has been removed from the website, as the form manager software it relied on will no longer be supported by our institution.
  • Update glossary to differentiate between structural and functional genome annotation.

This release is archived on Zenodo: https://doi.org/10.5281/zenodo.14049736

List of merged pull requests since v1.3.0

Full Changelog: https://github.com/ScilifelabDataCentre/genome-portal/compare/v1.3.0...v1.3.1

- Python
Published by RMCrean 11 months ago

genome-portal - Swedish Reference Genome Portal v1.3.0

Notable content

  • Dark mode added to the portal with the ability to toggle/save your preference.
  • Other minor stylistic changes to make the UI more consistent.

This release is archived on Zenodo: https://doi.org/10.5281/zenodo.14049736

List of merged pull requests since v1.2.1 Full Changelog: https://github.com/ScilifelabDataCentre/genome-portal/compare/v1.2.1...v1.3.0

- Python
Published by RMCrean about 1 year ago

genome-portal - Swedish Reference Genome Portal v1.2.1

This third release of the Swedish Reference Genome Portal introduces a new species, Amphiura filiformis (a species of brittle star), to the portal alongside a mitochondrial assembly for Parnassius mnemosyne (Clouded Apollo butterfly).

Notable content

  • The species Amphiura filiformis (a species of brittle star) is introduced to the portal.
  • A mitochondrial genome assembly and an annotation track with mitochondrial genes are added to the genome browser of Parnassius mnemosyne (Clouded Apollo butterfly).
  • Pagination of species cards on the homepage (won't be visible until there are ≥8 species).

Developer tools

  • A GitHub contribution guide.
  • Improvements to the command line scripts that use Docker to build and serve the genome portal.
  • Generate assembly alias files as part of the data build step with make.

This release is archived on Zenodo: https://doi.org/10.5281/zenodo.14049736

List of merged pull requests since v1.1.0 Full Changelog: https://github.com/ScilifelabDataCentre/genome-portal/compare/v1.1.0...v1.2.1

Note: The release of v1.2.0 based on commit https://github.com/ScilifelabDataCentre/genome-portal/commit/32c91048ecab05a4c12a9508f770e7c990f97af2 was skipped due to a bug being found in the make file before it was released to production. Release v1.2.1 includes the bug fix.

- Python
Published by RMCrean about 1 year ago

genome-portal - Swedish Reference Genome Portal v1.1.0

This second release of the Swedish Reference Genome Portal introduces new functionality to the Portal and improved developer tools.

Notable content

  • copy-to-clipboard functionality throughout the website to facilitate the copying of citations and code blocks.

Developer tools

  • Work on displaying secondary assemblies in separate views.
  • Add end-2-end testing for the website using Playwright.
  • Setup our CI/CD processes for trunk based development.

This release is archived on Zenodo: https://doi.org/10.5281/zenodo.14049736

Full Changelog: https://github.com/ScilifelabDataCentre/genome-portal/compare/v1.0.0...v1.1.0

- Python
Published by RMCrean about 1 year ago

genome-portal - Swedish Reference Genome Portal v1.0.0

This first release of the Swedish Reference Genome Portal introduces 6 species together with 44 annotation tracks, visualized with JBrowse version 2.15.4.

Introduced species

  • Meganyctiphanes norvegica, Northern krill
  • Parnassius mnemosyne, Clouded apollo butterfly
  • Skeletonema marinoi R05AC, A diatom species
  • Littorina saxatilis, Rough periwinkle
  • Linum tenue Desf., A species of flax
  • Linum trigynum L., French Flax

Notable content

Aside from the species-specific information, this release includes: - Detailed citation guidelines - User guide and FAQ - Glossary - Contribution guidelines

Developer tools

Under the scripts directory, you will find: - add_new_species.py to ease the addition of new species - dockerbuild to build our Docker images - dockerserve to run the website locally - dockermake to prepare the genomic data and configure JBrowse to display it

This release is archived on Zenodo: https://doi.org/10.5281/zenodo.14049736

- Python
Published by kwentine over 1 year ago